[English] 日本語
Yorodumi
- EMDB-66032: Cryo-EM structure of the GarQ-lmYZ complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66032
TitleCryo-EM structure of the GarQ-lmYZ complex
Map data
Sample
  • Complex: Man-PTS from Lactococcus garvieae
    • Protein or peptide: Mannose/fructose/sorbose family PTS transporter subunit IIC
    • Protein or peptide: PTS mannose family transporter subunit IID
    • Protein or peptide: Prepeptide GarQ
  • Ligand: alpha-D-mannopyranose
Keywordsantibiotic resistance / antimicrobial peptides / mannose phosphotransferase system / Man-PTS / bacteriocins / non-pediocin-like/class IId bacteriocins / Garvicin Q / GarQ / MEMBRANE PROTEIN
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / defense response to bacterium / extracellular region / plasma membrane
Similarity search - Function
Bacteriocin, class IId / Lactococcin-like family / Bacteriocin-type signal sequence / Phosphotransferase system, mannose/fructose/sorbose family, IIC subunit / Phosphotransferase system, mannose/fructose/sorbose family IID component / PTS system sorbose-specific iic component / PTS system mannose/fructose/sorbose family IID component / PTS_EIIC type-4 domain profile. / PTS_EIID domain profile. / :
Similarity search - Domain/homology
PTS mannose family transporter subunit IID / Prepeptide GarQ / Mannose/fructose/sorbose family PTS transporter subunit IIC
Similarity search - Component
Biological speciesLactococcus garvieae (lactic acid bacteria) / Listeria monocytogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsWang JW
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371254 China
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: To Be Published
Title: Structural basis for the broad-spectrum antimicrobial activity of Garvicin Q
Authors: Wang JW
History
DepositionAug 31, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_66032.png

Downloads & links

-
Map

FileDownload / File: emd_66032.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.995 Å		1.07 Å/pix.
x 256 pix.
= 274.995 Å		1.07 Å/pix.
x 256 pix.
= 274.995 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.0360432 - 3.4434671
Average (Standard dev.)-0.001322056 (±0.1029827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.9952 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_66032_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_66032_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Man-PTS from Lactococcus garvieae

EntireName: Man-PTS from Lactococcus garvieae
Components
  • Complex: Man-PTS from Lactococcus garvieae
    • Protein or peptide: Mannose/fructose/sorbose family PTS transporter subunit IIC
    • Protein or peptide: PTS mannose family transporter subunit IID
    • Protein or peptide: Prepeptide GarQ
  • Ligand: alpha-D-mannopyranose

-
Supramolecule #1: Man-PTS from Lactococcus garvieae

SupramoleculeName: Man-PTS from Lactococcus garvieae / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Lactococcus garvieae (lactic acid bacteria)

-
Macromolecule #1: Mannose/fructose/sorbose family PTS transporter subunit IIC

MacromoleculeName: Mannose/fructose/sorbose family PTS transporter subunit IIC
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 27.377561 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVISIILVV LIAFLAGIEG ILDEFQFHQP LIACTLIGLV TGNLTACIIL GGTLQMIALG WANIGAAVAP DAALASVASA IILVLGGQG VAGIPSAIAI AIPLAVAGLF LTMIVRTLAV PIVHLMDRAA EKGNIRSVEW LHISAICMQG IRIAIPAAAL L FIPADSVQ ...String:
MSVISIILVV LIAFLAGIEG ILDEFQFHQP LIACTLIGLV TGNLTACIIL GGTLQMIALG WANIGAAVAP DAALASVASA IILVLGGQG VAGIPSAIAI AIPLAVAGLF LTMIVRTLAV PIVHLMDRAA EKGNIRSVEW LHISAICMQG IRIAIPAAAL L FIPADSVQ SFLEAMPAWL TDGMAIGGGM VVAVGYALVI NMMATKEVWP FFVIGFVVAA ISQLTLIAIG ALGVALALIY LN LSKMGGG NSNGGGGGNS RDPLGDILND Y

UniProtKB: Mannose/fructose/sorbose family PTS transporter subunit IIC

-
Macromolecule #2: PTS mannose family transporter subunit IID

MacromoleculeName: PTS mannose family transporter subunit IID / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 33.402164 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAEKIELSKR DRLRVAWRST FIQGSWNYER MQNGGWAFSM IPAIKKLYKT KEDRSSALKR HLEFFNTHPY IASPILGVTL ALEEERANG AEVDDVAIQG VKVGMMGPLA GVGDPVFWFT IRPMLGALGA SLALSGNILG PILFFVAWNV IRWGFMWYTQ E FGYKAGSK ...String:
MAEKIELSKR DRLRVAWRST FIQGSWNYER MQNGGWAFSM IPAIKKLYKT KEDRSSALKR HLEFFNTHPY IASPILGVTL ALEEERANG AEVDDVAIQG VKVGMMGPLA GVGDPVFWFT IRPMLGALGA SLALSGNILG PILFFVAWNV IRWGFMWYTQ E FGYKAGSK ITDDLSGGLL QDITKGASIL GMFVLAALVQ RWVNIQFAPI ISKVKLDEGA YIDWSHLPQG AQGIKTALQQ QQ AGLALSE IKVTTLQNNL DNLIPGLAAV ALTFLCMWLL KKKISPIIII LGLFVVGIVG HLIGLL

UniProtKB: PTS mannose family transporter subunit IID

-
Macromolecule #3: Prepeptide GarQ

MacromoleculeName: Prepeptide GarQ / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lactococcus garvieae (lactic acid bacteria)
Molecular weightTheoretical: 5.349951 KDa
Recombinant expressionOrganism: Lactococcus phage phiL47 (virus)
SequenceString:
EYHLMNGANG YLTRVNGKYV YRVTKDPVSA VFGVISNGWG SAGAGFGPQH

UniProtKB: Prepeptide GarQ

-
Macromolecule #4: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 55270
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more